LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file

# run the first part and write out restart
include in.template-mix
# demo for atom style template simulating a cyclohexane methane mixture
# part 1: creating system with create_atoms

units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
LAMMPS molecule file. Cyclohexane(UA)
  1 molecules
  0 fragments
  6 atoms with max type 1
  6 bonds with max type 1
  6 angles with max type 1
  6 dihedrals with max type 1
  0 impropers with max type 0
atom_style template cychex

pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic

lattice sc 6.0
Lattice spacing in x,y,z = 6 6 6
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1
Created orthogonal box = (-24 -24 -24) to (24 24 24)
  1 by 2 by 2 MPI processor grid

create_atoms 0 box mol cychex 734594
Created 3072 atoms
  using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
  create_atoms CPU = 0.001 seconds
create_atoms 2 random 800 495437 box
Created 800 atoms
  using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
  create_atoms CPU = 0.000 seconds

mass 1 14.027
mass 2 16.043

pair_coeff 1 1  0.1180  3.905
pair_coeff 2 2  0.2940  3.730

bond_coeff      1  260.00 1.5260
angle_coeff     1  63.0   112.40
dihedral_coeff  1  2.0 1 3

thermo 100
minimize 0.001 0.001 500 1000
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 7 7 7
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.345 | 5.441 | 5.728 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0              7.5430044e+16  341.92144      7.5430044e+16  1.8707026e+17
       100   0             -3410.6986      572.28283     -2838.4158      14603.831    
       200   0             -6109.2306      483.67771     -5625.5529      5069.1821    
       204   0             -6137.0238      483.1464      -5653.8774      4952.4083    
Loop time of 0.719475 on 4 procs for 204 steps with 3872 atoms

99.6% CPU use with 4 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final = 
    7.54300441078755e+16  -5648.75822666276  -5653.87742467986
  Force two-norm initial, final = 8.7430661e+18 74.636836
  Force max component initial, final = 4.1468626e+18 8.680078
  Final line search alpha, max atom move = 0.0032186724 0.027938327
  Iterations, force evaluations = 204 328

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.59281    | 0.6027     | 0.60956    |   0.8 | 83.77
Bond    | 0.018776   | 0.020785   | 0.026388   |   2.2 |  2.89
Neigh   | 0.054209   | 0.054242   | 0.054273   |   0.0 |  7.54
Comm    | 0.018189   | 0.03064    | 0.042206   |   4.9 |  4.26
Output  | 3.3034e-05 | 3.5624e-05 | 4.3263e-05 |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.01107    |            |       |  1.54

Nlocal:            968 ave         980 max         954 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost:           6630 ave        6644 max        6616 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs:         193550 ave      195957 max      191376 min
Histogram: 2 0 0 0 0 0 0 0 1 1

Total # of neighbors = 774200
Ave neighs/atom = 199.94835
Ave special neighs/atom = 3.9669421
Neighbor list builds = 14
Dangerous builds = 0
reset_timestep 0

velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.22 | 4.507 | 4.603 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   100           -6137.0238      483.1464      -4500.0059      5429.3515    
       100   107.18608     -5623.5468      925.13787     -3461.6193      5640.5922    
       200   119.37771     -5671.054       1050.9081     -3242.6804      7494.8576    
       300   127.21216     -5646.3171      1053.2825     -3125.1696      5661.5841    
       400   133.87894     -5674.4359      1139.3079     -2990.337       7202.7       
       500   138.76354     -5679.3297      1234.4508     -2843.7258      6745.1519    
       600   150.51628     -5665.2143      1210.3078     -2718.142       6301.1312    
       700   152.13291     -5680.6166      979.71444     -2945.4837      8424.0062    
       800   161.60449     -5579.521       1209.1388     -2505.674       5226.3319    
       900   177.80597     -5626.7406      1125.8767     -2449.2113      9035.9218    
      1000   181.98782     -5509.1736      924.24027     -2485.0276      5775.8317    
      1100   189.93412     -5534.8176      1169.5911     -2173.6307      8072.3434    
      1200   194.04459     -5508.0919      1169.0571     -2100.0095      7766.2625    
      1300   203.40621     -5400.0439      1229.5897     -1823.4077      6533.8169    
      1400   211.36099     -5362.2808      1318.5794     -1604.867       9789.8496    
      1500   221.24251     -5263.1861      1410.6972     -1299.6344      6407.5052    
      1600   234.83277     -5316.3854      1299.4287     -1307.2882      10199.28     
      1700   233.61193     -5187.0022      1246.0158     -1245.4048      7482.5096    
      1800   247.00713     -5193.2051      1451.1363     -891.92372      9836.6864    
      1900   250.10386     -5165.7314      1259.876      -1019.978       8648.7513    
      2000   257.7022      -5083.7142      1486.9813     -623.18058      9076.3674    
      2100   273.9293      -5061.7945      1463.3978     -437.60445      10039.49     
      2200   276.40166     -4948.9281      1538.5962     -221.01165      9013.3961    
      2300   287.28669     -5039.6841      1535.7768     -188.98782      10739.853    
      2400   290.35344     -4947.2095      1615.8983      18.994602      8326.4501    
      2500   305.29351     -4925.5822      1669.8823      266.99522      11465.135    
Loop time of 4.32742 on 4 procs for 2500 steps with 3872 atoms

Performance: 49.914 ns/day, 0.481 hours/ns, 577.711 timesteps/s, 2.237 Matom-step/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.7864     | 3.836      | 3.8948     |   2.2 | 88.64
Bond    | 0.13058    | 0.13362    | 0.13735    |   0.8 |  3.09
Neigh   | 0.13597    | 0.13601    | 0.13605    |   0.0 |  3.14
Comm    | 0.12304    | 0.18542    | 0.23763    |  10.5 |  4.28
Output  | 0.00033524 | 0.00036705 | 0.00045513 |   0.0 |  0.01
Modify  | 0.027504   | 0.027917   | 0.028571   |   0.3 |  0.65
Other   |            | 0.008118   |            |       |  0.19

Nlocal:            968 ave         986 max         944 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost:        6379.75 ave        6407 max        6352 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs:         192584 ave      196718 max      188693 min
Histogram: 1 1 0 0 0 0 0 1 0 1

Total # of neighbors = 770338
Ave neighs/atom = 198.95093
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0
#write_data template-mix.data
#write_restart template-mix.restart
write_restart template-mix.restart
System init for write_restart ...
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule

# now restart
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
molecule cychex cyclohexane.mol
Read molecule template cychex:
LAMMPS molecule file. Cyclohexane(UA)
  1 molecules
  0 fragments
  6 atoms with max type 1
  6 bonds with max type 1
  6 angles with max type 1
  6 dihedrals with max type 1
  0 impropers with max type 0
read_restart template-mix.restart
Reading restart file ...
  restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024
  restoring atom style template from restart
  orthogonal box = (-24 -24 -24) to (24 24 24)
  1 by 2 by 2 MPI processor grid
  restoring pair style lj/cut from restart
  restoring bond style harmonic from restart
  restoring angle style harmonic from restart
  restoring dihedral style harmonic from restart
  3872 atoms
  3072 template bonds
  3072 template angles
  3072 template dihedrals
  read_restart CPU = 0.001 seconds

thermo 100

fix 1 all nvt temp 300.0 300.0 1.0
Resetting global fix info from restart file:
  fix style: nvt, fix ID: 1
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
All restart file global fix info was re-assigned
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 7 7 7
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.192 | 4.288 | 4.574 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
      2500   305.29351     -4925.5822      1669.8823      266.99522      11465.135    
      2600   296.63161     -4937.8377      1616.2295      101.13964      8654.8533    
      2700   303.79396     -4951.8442      1732.7298      286.27771      11140.127    
      2800   297.39677     -4879.1242      1642.1355      194.58806      8993.2494    
      2900   299.13542     -4888.1435      1660.1105      223.60558      10716.3      
      3000   298.07888     -4928.2353      1650.6616      161.87369      10088.459    
      3100   304.09536     -4901.4853      1614.3116      221.69625      9505.2057    
      3200   301.51357     -4930.5129      1628.4386      177.00496      11411.933    
      3300   297.45744     -4923.6217      1700.537       209.19205      8189.571     
      3400   298.52831     -5012.7313      1736.6929      168.59495      11673.119    
      3500   295.66767     -4947.4296      1700.0072      164.20283      8222.3067    
      3600   296.7267      -5112.3707      1727.4319      38.906285      10608.481    
      3700   302.92855     -4994.4012      1789.7274      290.73255      8829.4479    
      3800   296.77191     -5034.2589      1657.2635      47.371248      9968.3521    
      3900   299.86962     -4972.7385      1744.2808      231.65266      10076.37     
      4000   304.89527     -5011.2464      1664.6779      171.53137      8926.0386    
      4100   296.81738     -5013.2169      1727.5801      139.25455      10898.733    
      4200   300.67532     -4988.3547      1782.1574      263.20975      8164.1158    
      4300   297.74901     -5023.3433      1784.7361      197.03396      11344.862    
      4400   302.0571      -5033.3547      1723.2662      175.26243      8016.975     
      4500   305.31958     -5062.5597      1767.0048      227.44095      10827.294    
Loop time of 3.5798 on 4 procs for 2000 steps with 3872 atoms

Performance: 48.271 ns/day, 0.497 hours/ns, 558.691 timesteps/s, 2.163 Matom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.0514     | 3.1162     | 3.2058     |   3.3 | 87.05
Bond    | 0.10377    | 0.10776    | 0.11194    |   1.0 |  3.01
Neigh   | 0.14121    | 0.14125    | 0.1413     |   0.0 |  3.95
Comm    | 0.092144   | 0.18542    | 0.25437    |  14.1 |  5.18
Output  | 0.00025632 | 0.00028151 | 0.00035298 |   0.0 |  0.01
Modify  | 0.02193    | 0.022227   | 0.022584   |   0.2 |  0.62
Other   |            | 0.006618   |            |       |  0.18

Nlocal:            968 ave         984 max         948 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost:         6349.5 ave        6370 max        6330 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs:         192457 ave      196654 max      187154 min
Histogram: 1 0 0 0 1 0 0 0 1 1

Total # of neighbors = 769828
Ave neighs/atom = 198.81921
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0

# clean up
shell rm template-mix.restart
Total wall time: 0:00:08
